I know there were multiple reports of issues when using TheDarkWraith_DC_Water_Disturbance_v4_0_SH3
and someone - I think it was Stiebler - did some testing and determined that there was a problem with corrupted saved games while using that mod. He pretty much narrowed it down to that mod in particular. There was a discussion about it in the Mods Workshop forum I think but I don't know if it was a separate thread or just came up in a general "saved games CTD please help" thread like we get from time to time.
However I don't recall it being a question of how long a system was shut down in between saving and reloading, or of saves working one time and then CTDing the next.
All things considered, if you're going to start disabling mods to try and find the problem I'd certainly start with that one since it is known to cause a problem with saved games once something happens in the course of playing that activates whatever effect it creates.
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